Jin-Yuan Liu

Tsinghua University, Peping, Beijing, China

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Publications (50)178.67 Total impact

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    Zebin Wang · Feng Wang · Rui Duan · Jin-Yuan Liu

    Full-text · Dataset · Jan 2016
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    Yuan Yao · Bing Zhang · Chun-Juan Dong · Ying Du · Lin Jiang · Jin-Yuan Liu
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    ABSTRACT: To explore lint fiber initiation-related proteins in allotetraploid cotton (Gossypium hirsutum L.), a comparative proteomic analysis was performed between wild-type cotton (Xu-142) and its fuzzless-lintless mutant (Xu-142-fl) at five developmental time points for lint fiber initiation from -3 to +3 days post-anthesis (dpa). Using two-dimensional gel electrophoresis (2-DE) combined with mass spectrometry (MS) analyses, 91 differentially accumulated protein (DAP) species that are related to fiber initiation were successfully identified, of which 58 preferentially accumulated in the wild-type and 33 species in the fl mutant. These DAPs are involved in various cellular and metabolic processes, mainly including important energy/carbohydrate metabolism, redox homeostasis, amino acid and fatty acid biosynthesis, protein quality control, cytoskeleton dynamics, and anthocyanidin metabolism. Further physiological and biochemical experiments revealed dynamic changes in the carbohydrate flux and H2O2 levels in the cotton fiber initiation process. Compared with those in the fl mutant, the contents of glucose and fructose in wild-type ovules sharply increased after anthesis with a relatively higher rate of amino acid biosynthesis. The relative sugar starvation and lower rate of amino acid biosynthesis in the fl mutant ovules may impede the carbohydrate/energy supply and cell wall synthesis, which is consistent with the proteomic results. However, the H2O2 burst was only observed in the wild-type ovules on the day of anthesis. Cotton boll injection experiments in combination with electron microscope observation collectively indicated that H2O2 burst, which is negatively regulated by ascorbate peroxidases (APx), plays an important role in the fiber initiation process. Taken together, our study demonstrates a putative network of DAP species related to fiber initiation in cotton ovules and provides a foundation for future studies on the specific functions of these proteins in fiber development.
    Full-text · Article · Feb 2015 · PLoS ONE
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    Full-text · Article · Aug 2014 · Molecular Plant
  • Dingwei Yu · Yanmei Wang · Wei Xue · Shuli Fan · Shuxun Yu · Jin-Yuan Liu
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    ABSTRACT: MicroRNAs (miRNAs) are endogenous, non-coding small RNAs that play crucial regulatory roles in the regulation of gene expression in plants. Our previous studies have identified several dozens of miRNAs related to fiber initiation and elongation in cotton (Gossypium hirsutum). Here, some important miRNAs involved in fiber secondary wall thickening were further investigated. A small RNA library was constructed from cotton fibers sampled at 25 days post anthesis (dpa) and subjected to high-throughput sequencing. Computational analysis detected the expression of 98 known miRNA families and 21 novel miRNA candidates in secondary wall thickening fiber cells. Comparative profiling of the known and novel miRNAs with previously reported small RNA data derived from elongating fibers revealed 16 up-regulated and 22 down-regulated miRNAs with more than 2-fold changes related to secondary wall thickening. Furthermore, target predictions for the 38 differentially expressed miRNAs resulted in 299 putative target genes, some of which were found to be involved in the regulation of important cell processes such as transcription regulation, energy metabolism, electron transport, stress response, and signal transduction. The results of our study provide valuable information for further functional investigations of the important miRNAs involved in cotton fiber secondary wall thickening.
    No preview · Article · Aug 2014 · Journal of Genetics and Genomics
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    Wei Xue · Zhengming Wang · Mingjian Du · Yidi Liu · Jin-Yuan Liu
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    ABSTRACT: MicroRNAs (miRNAs) and other types of small regulatory RNAs play critical roles in the regulation of gene expression at the post-transcriptional level in plants. Cotton is one of the most economically important crops, but little is known about the roles of miRNAs during cotton fiber elongation. Here, we combined high-throughput sequencing with computational analysis to identify small RNAs (sRNAs) related to cotton fiber elongation in Gossypium hirsutum L. (G. hirsutum). The sequence analysis confirmed the expression of 79 known miRNA families in elongating fiber cells and identified 257 novel miRNAs, primarily derived from corresponding specific loci in the Gossypium raimondii Ulbr. (G. raimondii) genome. Furthermore, a comparison of the miRNAomes revealed that 46 miRNA families were differentially expressed throughout the elongation period. Importantly, the predicted and experimentally validated targets of eight miRNAs were associated with fiber elongation, with obvious functional relationships with calcium and auxin signal transduction, fatty acid metabolism, anthocyanin synthesis and the xylem tissue differentiation. Moreover, one tasiRNA was also identified, and its target, ARF4, was experimentally validated in vivo. This study not only facilitated the discovery of 257 novel low-abundance miRNAs in elongating cotton fiber cells but also revealed a potential regulatory network of nine sRNAs important for fiber elongation. The identification and characterization of miRNAs in elongating cotton fiber cells might promote the further study of fiber miRNA regulation mechanisms and provide insight into the importance of miRNAs in cotton.
    Preview · Article · Sep 2013 · BMC Genomics
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    Bing Zhang · Yi-Wei Yang · Yu Zhang · Jin-Yuan Liu
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    ABSTRACT: In our previous study, we used a comparative proteomic approach based on 2-DE to profile dynamic proteomes of cotton fibers and found 235 protein spots differentially expressed during the elongation process ranging from 5 to 25 days post-anthesis (DPA). Of them, only 106 differentially expressed proteins (DEPs) were identified by mass spectrometry due to database limitations at the time. In the present work, we successfully identified the remaining 129 DEPs from the same experimental system using high-resolution mass spectrometry with an updated database. Bioinformatic analysis revealed that proteins involved in carbohydrate and protein metabolism, transport, and redox homeostasis are the most abundant, and glycolysis was found to be the most significantly regulated process during fiber elongation. Our high-confidence reference dataset, composed of 235 DEPs, provides a valuable resource for future studies on the molecular mechanism of cotton fiber elongation.
    Full-text · Article · Apr 2013 · Proteomics
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    Bing Zhang · Jin-Yuan Liu
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    ABSTRACT: Two-dimensional gel electrophoresis (2-DE)-based proteomics approach was applied to extensively explore the molecular basis of plant development and environmental adaptation. These proteomics analyses revealed thousands of differentially expressed proteins (DEPs) closely related to different biological processes. However, little attention has been paid to how peptide mass fingerprinting (PMF) data generated by the approach can be directly utilized for the determination of protein phosphorylation. Here, we used the software tool FindMod to predict the peptides that might carry the phosphorylation modification by examining their PMF data for mass differences between the empirical and theoretical peptides and then identified phosphorylation sites using MALDI TOF/TOF according to predicted peptide data from these DEP spots in the 2-D gels. As a result, a total of 48 phosphorylation sites of 40 DEPs were successfully identified among 235 known DEPs previously revealed in the 2-D gels of elongating cotton fiber cells. The 40 phosphorylated DEPs, including important enzymes such as enolase, transketolase and UDP-L-rhamnose synthase, are presumed to participate in the functional regulation of numerous metabolic pathways, suggesting the reverse phosphorylation of these proteins might play important roles in elongating cotton fibers. The results also indicated that some different isoforms of the identical DEP revealed in our 2-DE-based proteomics analysis could be annotated by phosphorylation events. Taken together, as the first report of large-scale identification of phosphorylation sites in elongating cotton fiber cells, our study provides not only an excellent example of directly identifying phosphorylation sites from known DEPs on 2-D gels but also provides a valuable resource for future functional studies of phosphorylated proteins in this field.
    Full-text · Article · Mar 2013 · PLoS ONE
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    ABSTRACT: In this study, a comparative proteomic analysis was employed to identify fuzz fiber initiation-related proteins in wild-type diploid cotton (Gossypium arboreum L.) and its fuzzless mutant. Temporal changes in global proteomes were examined using 2-DE at five developmental time points for fuzz fiber initiation, and 71 differentially expressed protein species were identified by MS, 45 of which were preferentially accumulated in the wild-type. These proteins were assigned to several functional categories, mainly in cell response/signal transduction, redox homeostasis, protein metabolism and energy/carbohydrate metabolism. It was remarkable that more than ten key proteins with high-abundance were involved in gibberellic acid (GA) signaling and ROS scavenging, and increasing concentrations of active GAs and H2O2 were also detected approximately 5 dpa in wild type ovules. Furthermore, in vivo GA and H2O2 treatments of ovules inside young bolls showed that these compounds can synergistically promote fuzz fiber initiation. Our findings not only described a dynamic protein network supporting fuzz initiation in diploid cotton fiber ovules, but also deepened our understanding of the molecular basis of cotton fiber initiation.
    Full-text · Article · Mar 2013 · Journal of proteomics
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    Xueping Wu · Yongsheng Cheng · Tian Li · Zhao Wang · Jin-Yuan Liu
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    ABSTRACT: The functional characterization of novel transcription factors identified by systematic analysis remains a major challenge due to insufficient data to interpret their specific roles in signaling networks. Here we present a DNA-binding sequence discovery method to in vitro identify a G-rich, 11-bp DNA-binding motif of a novel potential transcription factor AtYY1, a zinc finger protein in Arabidopsis, by using polymerase chain reaction-assisted in vitro selection and surface plasmon resonance analysis. Further mutational analysis of the conserved G bases of the potential motif confirmed that AtYY1 specifically bound to these conserved G sites. Additionally, genome-wide target gene analysis revealed that AtYY1 was involved in diverse cellular pathways, including glucose metabolism, photosynthesis, phototropism, and stress response.
    Preview · Article · Apr 2012 · Acta Biochimica et Biophysica Sinica
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    ABSTRACT: An increasing number of microRNAs (miRNAs) have been shown to play crucial regulatory roles in the process of plant development. Here, we used high-throughput sequencing combined with computational analysis to characterize miRNAomes from the ovules of wild-type upland cotton and a fiberless mutant during fiber initiation. Comparative miRNAome analysis combined with northern blotting and RACE-PCR revealed seven fiber initiation-related miRNAs expressed in cotton ovules and experimentally validated targets of these miRNAs are involved in different cellular responses and metabolic processes, including transcriptional regulation, auxin and gibberellin signal transduction, actin bundles, and lignin biosynthesis. This paper describes a complex regulatory network consisting of these miRNAs expressed in cotton ovules to coordinate fiber initiation responses. In addition, 36 novel miRNAs and two conserved miRNAs were newly identified, nearly doubling the number of known cotton miRNA families to a total of 78. Furthermore, a chromatin remodeling complex subunit and a pre-mRNA splicing factor are shown for the first time to be miRNA targets. To our knowledge, this study is the first systematic investigation of fiber initiation-related miRNAs and their targets in the developing cotton ovule, deepening our understanding of the important regulatory functions of miRNAs in cotton fiber initiation.
    Preview · Article · Dec 2011 · Molecular Plant
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    Dataset: Table S4
    Lu Zhou · Saleem A. Bokhari · Chun-Juan Dong · Jin-Yuan Liu
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    ABSTRACT: Localization prediction of proteins without signal sequences by the SecretomeP software. (DOCX)
    Preview · Dataset · Feb 2011
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    Dataset: File S2
    Lu Zhou · Saleem A. Bokhari · Chun-Juan Dong · Jin-Yuan Liu
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    ABSTRACT: Supplemental spectra MS/MS. Annotated spectra of 21 differentially expressed protein spots identified by MS/MS. (PPT)
    Preview · Dataset · Feb 2011
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    Dataset: Figure S1
    Lu Zhou · Saleem A. Bokhari · Chun-Juan Dong · Jin-Yuan Liu
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    ABSTRACT: Proteins identified related with carbohydrate metabolism and redox homeostasis in response to H2O2. (DOCX)
    Preview · Dataset · Feb 2011
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    Lu Zhou · Saleem A Bokhari · Chun-Juan Dong · Jin-Yuan Liu
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    ABSTRACT: Plant apoplast is the prime site for signal perception and defense response, and of great importance in responding to environmental stresses. Hydrogen peroxide (H(2)O(2)) plays a pivotal role in determining the responsiveness of cells to stress. However, how the apoplast proteome changes under oxidative condition is largely unknown. In this study, we initiated a comparative proteomic analysis to explore H(2)O(2)-responsive proteins in the apoplast of rice seedling roots. 14-day-old rice seedlings were treated with low concentrations (300 and 600 ┬ÁM) of H(2)O(2) for 6 h and the levels of relative electrolyte leakage, malondialdehyde and H(2)O(2) were assayed in roots. The modified vacuum infiltration method was used to extract apoplast proteins of rice seedling roots, and then two-dimensional electrophoresis gel analysis revealed 58 differentially expressed protein spots under low H(2)O(2) conditions. Of these, 54 were successfully identified by PMF or MS/MS as matches to 35 different proteins including known and novel H(2)O(2)-responsive proteins. Almost all of these identities (98%) were indeed apoplast proteins confirmed either by previous experiments or through publicly available prediction programs. These proteins identified are involved in a variety of processes, including redox homeostasis, cell wall modification, signal transduction, cell defense and carbohydrate metabolism, indicating a complex regulative network in the apoplast of seedling roots under H(2)O(2) stress. The present study is the first apoplast proteome investigation of plant seedlings in response to H(2)O(2) and may be of paramount importance for the understanding of the plant network to environmental stresses. Based on the abundant changes in these proteins, together with their putative functions, we proposed a possible protein network that provides new insights into oxidative stress response in the rice root apoplast and clues for the further functional research of target proteins associated with H(2)O(2) response.
    Full-text · Article · Feb 2011 · PLoS ONE
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    Dataset: Table S5
    Lu Zhou · Saleem A. Bokhari · Chun-Juan Dong · Jin-Yuan Liu
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    ABSTRACT: List of common proteins in the rice apoplast proteome under different treatments. (DOCX)
    Preview · Dataset · Feb 2011
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    Dataset: Figure S3
    Lu Zhou · Saleem A. Bokhari · Chun-Juan Dong · Jin-Yuan Liu
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    ABSTRACT: Schematic structure of the At-RLK3 protein and the RLP protein we identified (OsRMC). (DOCX)
    Preview · Dataset · Feb 2011
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    Dataset: Table S1
    Lu Zhou · Saleem A. Bokhari · Chun-Juan Dong · Jin-Yuan Liu
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    ABSTRACT: Differentially expressed protein spots identified by PMF or MS/MS. (DOCX)
    Preview · Dataset · Feb 2011
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    Dataset: File S1
    Lu Zhou · Saleem A. Bokhari · Chun-Juan Dong · Jin-Yuan Liu
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    ABSTRACT: Supplemental spectra PMF. Annotated spectra for 33 differentially expressed protein spots identified by PMF. (PPT)
    Preview · Dataset · Feb 2011
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    Dataset: Figure S2
    Lu Zhou · Saleem A. Bokhari · Chun-Juan Dong · Jin-Yuan Liu
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    ABSTRACT: Hierarchical clustering of H2O2-responsive proteins associated with carbohydrate metabolism (A) and redox regulation (B). (DOCX)
    Preview · Dataset · Feb 2011
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    Dataset: Table S3
    Lu Zhou · Saleem A. Bokhari · Chun-Juan Dong · Jin-Yuan Liu
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    ABSTRACT: Redundancy of differentially displayed protein spots identified by PMF or MS/MS. (XLS)
    Preview · Dataset · Feb 2011

Publication Stats

1k Citations
178.67 Total Impact Points

Institutions

  • 2002-2015
    • Tsinghua University
      • School of Life Sciences
      Peping, Beijing, China
  • 2009
    • University of California, Riverside
      • Department of Botany and Plant Sciences
      Riverside, California, United States